Targeted Proteomics Data
Targeted proteomics analysis was conducted on cerebrospinal fluid and blood plasma of both Parkinson's Disease patients and healthy participants in the PPMI cohort. Analysis was conducted using Olink Explore which uses two DNA tagged antibodies per analyte and amplification in a Proximity Extension Assay (PEA) for measuring protein levels. The method requires data to be converted into Normalized protein expression (NPX) values to be used in downstream analysis. NPX data is then intensity normalized and undergoes extensive quality control using the different assay controls before proceeding with analysis .
AMP PD Release 2.5 contains data generated from 743 matched CSF and Plasma samples from 212 participants. The data includes a preview of Olink Explore 138 participants run on 521 CSF samples & 521 matched plasma samples PDBP and 74 participants run on 222 CSF samples & 222 matched plasma samples from PPMI. These data will be fully integrated with untargeted proteomics in the AMP PD 3.0 release with additional supporting materials.
What's on this page:
Baseline | 6M | 12M | 18M | 24M | 36M | 48M | 60M | 84M | 96M | Total | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|
PDBP | Plasma | 111 | 2 | 91 | 28 | 114 | 110 | 48 | 17 | 0 | 0 | 521 |
CSF | 111 | 2 | 91 | 28 | 114 | 110 | 48 | 17 | 0 | 0 | 521 | |
PPMI | Plasma | 74 | 15 | 17 | 0 | 35 | 21 | 53 | 4 | 2 | 1 | 222 |
CSF | 74 | 15 | 17 | 0 | 35 | 21 | 53 | 4 | 2 | 1 | 222 |
Sample Selection Criteria
The criteria used to select these samples were as follows:
- Samples for three timepoint or more available
- Participant samples selected were from participants who had previously generated corresponding Whole Genome Sequencing or Transcriptomic data on the AMP PD Knowledge Platform
- All CSF samples selected had hemoglobin < 100 ng/mL to assure limited blood contamination
- All Plasma and CSF samples were collected under similar protocols
AMP PD Quality control of the preview release data was performed by Victoria Dardov from Technome as part of a contract with the Foundation for the National Institutes of Health (FNIH).
Information here was prepared by the Olink Proteomics in consultation with the AMP PD Proteomics Working Group.
Method
Proximity Extension Assay for Targeted Proteomics
Normalized Protein Expression (NPX) quantifies the relative amount of a specific protein. This is determined by performing an immunoassay for a targeted protein. Antibodies that bind to a protein of interest contain unique sequences that are extended, amplified and subsequently detected and quantified by NGS. The amount of this sequence is normalized to standard plate controls to give relative quantities of targeted proteins.
Assay Controls Summary
Extensive quality control is performed for each assay in order to control and assess technical performance of the assay at each step. This ensures generation of reliable data.
AMP PD Controls
AMP-PD quality control further examines the data and includes sample, run and control sample QC.
Generating NPX values
The Explore system´s raw data output are NGS counts, where each combination of an assay and sample is given an integer value based on the number of DNA copies detected. These raw data counts are converted into NPX values for use in downstream statistical analysis.